Natural Compounds or Their Derivatives against Breast Cancer: A Computational Study

Background Breast cancer is one of the most common types of cancer diagnosed and the second leading cause of death among women. Breast cancer susceptibility proteins of type 1 and 2 are human tumor suppressor genes. Genetic variations/mutations in these two genes lead to overexpression of human breast tumor suppressor genes (e.g., BRCA1, BRCA2), which triggers uncontrolled duplication of cells in humans. In addition, multidrug resistance protein 1 (MDR1), an important cell membrane protein that pumps many foreign substances from cells, is also responsible for developing resistance to cancer chemotherapy. Aim of the Study. The aim of this study was to analyze some natural compounds or their derivatives as part of the development of strong inhibitors for breast cancer. Methodology. Molecular docking studies were performed using compounds known in the literature to be effective against BRCA1 and BRCA2 and MDR1, with positive control being 5-fluorouracil, an antineoplastic drug as a positive control. Results The binding affinity of the compounds was analyzed, and it was observed that they had a better binding affinity for the target proteins than the standard drug 5-fluorouracil. Among the compounds analyzed, α-hederin, andrographolide, apigenin, asiatic acid, auricular acid, sinularin, curcumin, citrinin, hispolon, nerol, phytol, retinol palmitate, and sclareol showed the best binding affinity energy to the BRCA1, BRCA2, and MDR1 proteins, respectively. Conclusions α-Hederin, andrographolide, apigenin, asiatic acid, auricular acid, hispolon, sclareol, curcumin, citrinin, and sinularin or their derivatives can be a good source of anticancer agents in breast cancer.


Introduction
Breast cancer is one of the common types of diagnosed cancers and the second prime cause of death among women in western countries [1] and develops from breast tissue [2]. Most of the breast cancers are sporadic (90-95%); between 5 and 10% can be attributed to genetic predisposition with patients having a strong family history of the disease [3,4].
BRCA1 and BRCA2 are also human tumor suppressor genes [6,12], designed to chromosome 17q21 which encodes a nuclear protein of 1863 amino acids [9] that regulate transcriptional activation, DNA repair, apoptosis, cell-cycle checkpoint control, and chromosomal remodeling [13]. On the other hand, BRCA2 located to chromosome 13q12-q13 [14] and coding for a protein of 3418 amino acids [15,16]. Of the breast cancer susceptibility genes which have been identified nowadays, BRCA1 and BRCA2 are the most fundamental "high-risk" genes with several cases of breast and ovarian cancer accounting for most of the families [17]. If BRCA1 or BRCA2 is damaged by a BRCA mutation, damaged DNA is not repaired properly, and this increases the risk for breast cancer [18,19]. P-glycoprotein 1 (P-gp1), encoded by multidrug resistance protein 1 (MDR1), is an important protein of the cell membrane that pumps many foreign substances out of cells.
Most of the initially responsive breast tumors acquire a multidrug resistance phenotype [20,21]. The development of a multidrug-resistant phenotype in metastatic breast cancer is primarily responsible for the failure of current treatment regimens [22,23]. Resistance to multiple drugs (MDR) is defined as efflux activity, which may decrease intracellular chemotherapeutic concentrations, thus explaining the failure of treatment in human cancers [24,25]. Consequently, P-gp overexpression is one of the main mechanisms behind decreased intracellular drug accumulation and development of MDR cancers [25,26].

Computational Methods
2.1. In Silico Prediction of Activity Spectra for Substances (PASS). Prediction of anticancer activity of 16 natural compounds was done with the help of computer program, PASS (prediction of activity spectra for substances). Software estimates predicted activity spectrum of a compound as probable activity (Pa) and probable inactivity (Pi) [38]. The prediction of activity is based on structure-activity relationship analysis of the training set containing more than 200,000 compounds exhibiting more than 3800 kinds of biological activities. The values of Pa and Pi vary between 0.000 and 1.000. Only activities with Pa > Pi are considered as possible for a particular compound. If Pa > 0:7, the probability of experimental pharmacological action is high and if 0:5 < Pa < 0:7, probability of experimental pharmacological action is less. If the value of Pa < 0:5, the chance of finding the activity experimentally is less, but it may indicate a chance of finding a new compound [39][40][41].

Ligand Preparation.
The main phytochemicals and one approved drug for breast cancer treatment were downloaded from PubChem in the SDF file format. PubChem is a database for chemical molecules [42] (Figure 1).
The system is maintained by the National Centre for Biotechnology Information (NCBI), a component of the National Library of Medicine. By using Gaussian view 09 and Chem3D Pro12.0 program packages [43], all internal energies of the ligands were optimized.  Figure 1: The chemical structure of the screened compounds.      [27], BRCA2 (3EU7) [28], and MDR1 (6C0V) [29] ( Figure 2) were collected from the Protein Data Bank (PDB) database [44]. For the purpose of energy minimization crystal structure, we utilized Swiss-PDB Viewer software package (version 4.1.0), and then, all the heteroatoms and water molecules of proteins are removed by using PyMOL (version 1.7.4.5) before docking [45]. Both the proteins and drug structures, for the analysis of docking results, are taken into PDBQT format finally [46].

Docking Analysis and Determination of Binding Site.
In in silico study, molecular docking is a brilliant instrument which is used for predicting the drugs candidate's pharmacodynamics profile by scoring and orienting them to the receptor binding sites [47]. Docking result determines the measure of ligand interaction to the active site of the targeted protein.

Conclusion
It can be concluded from the overall study that α-hederin, andrographolide, apigenin, asiatic acid, auricularic acid, and sinularin have potent inhibitory activity against cancer proteins (BRCA1, BRCA2, and MDR1) compared to the other compounds. All the compounds exhibited significant binding energies and the noncovalent bonds compared to the other compounds. Nevertheless, α-hederin, andrographolide, apigenin, asiatic acid, auricularic acid, and sinularin successfully docked with BRCA1, BRCA2, and MDR1 proteins as these compounds have the activity for inhibiting cancer. The nonbonding interactions can effectively target the proteins for the inhibition of cancer. We have claimed from the overall studies that α-hederin, andrographolide, apigenin, asiatic acid, auricularic acid, and sinularin will be the best conformer for BRCA1, BRCA2, and MDR1conduced cancer for the future researchers. Our findings, in this way, could be manifested in clinical practice.

Data Availability
The data used to support the findings of this study are available from the corresponding author upon request.

Conflicts of Interest
The authors declare that they have no conflicts of interest.